mods have a download link that you click to download, once downloaded they either have an installer or you put them in the tech section, heres a basic example I download v-bros pack1 and so i copy it here(I'm going by what my folders are)
C:/program files/megaglest/techs/
if its a specific faction I want to add to the megapack(Elves for example) I'd copy it to this
C:/program files/megaglest/techs/megapack/factions/copy elves here
and I'd add there special resources tree and grace here
C:/program files/megaglest/techs/megapack/resources/copy tree and grace resources here.
I hope this is helpful, if not I'm sorry, if you need something clarified just ask.